Fermentation and Microbiome Research: Ancient Cultural Practices Meet Cutting Edge Genetic Analyses

By Sandor Ellix Katz

I call myself a fermentation revivalist.

It began twenty-some years ago as a personal obsession with all things fermented, starting with sauerkraut (my gateway) and continuing through yogurt, sourdough, and country wines into researching fermentation traditions around the world, and years of kitchen experimentation. I was drawn to the compelling flavors, the practical benefit of preservation, and the probiotic promise of live-culture foods. My obsession became a reputation, and led to an invitation to teach, and in that first workshop in 1998 I learned that for many people the prospect of cultivating bacteria on food is terrifying. Demystifying fermentation and showing people how easy, safe, fun, and delicious it is became a mission for me. Workshops led to books: Wild Fermentation, initially self-published in 2001, then expanded into a book and published by Chelsea Green in 2003, and about to be released in a revised and updated edition later this summer (2016); and the Art of Fermentation, much more in-depth, published in 2012.  The workshops have never stopped. I have not kept count, but there have been many hundreds of them, in nearly every state, and increasingly abroad.

There is great interest in fermentation, everywhere. People are interested in connecting with food, and cultural traditions, and agrarian practicality. And of course, most people love the flavors of fermentation. But more than anything, people are drawn to fermented foods and beverages for their perceived health benefits. Live culture foods such as yogurt and sauerkraut can improve digestion and overall immune function and contribute to well-being in myriad other ways, but in fact we know very little about how, and specifically about the interaction between the microbial communities of the fermented foods and the more complex microbial communities of our intestines.

I am not a scientist and have no formal background in biology (nor in food science or culinary arts). But via my interest in fermentation, I have become very interested in microbiology. The cultural practices of fermentation arose everywhere long before the science of microbiology (or for that matter the written word). But microbiology, and the new methods of genetic analysis, give us new insights into what is happening, and what we are learning is so exciting. Bacteria and other microscopic life forms are everywhere. They are in us and on us and everything we eat. They exist in elaborate communities with complexity we are just beginning to recognize and little comprehend.

I have followed microbiome research with great interest. I supported the initial American Gut Project crowdfunding, and submitted a sample for analysis. I have followed the work of Rob Knight, and we had a great conversation when we met at the San Diego Fermentation Festival in 2015. And I have visited Rachel Dutton’s lab and greatly admire her research on cheese. So when they approached me about testing foods I was fermenting, and the students fermenting them with me, I jumped at the chance.

In addition to all the workshops I travel to teach, I host residency programs at my home in Tennessee. These are intensive immersions into fermentation with 12-15 people, each of whom have at least some fermentation experience, over 5-6 days. Together we make and eat krauts and kimchis, yogurt, kefir, alcoholic beverages, lightly fermented soft drinks, koji (a Japanese starter culture), miso, tempeh, sourdoughs, dosas and idlis, injera, and more.

Sandor with students at Walnut Ridge.

One of these workshops was coming up just a few weeks after Rob and Rachel emailed me about collaborating. This was a great opportunity to test lots of varied fermented foods and beverages, at different stages of development, as well as people before, while, and after eating them intensively. The lab sent boxes of swabs, instructions, and we were off!

Each participant took three samples on arrival: stool, mouth, and (dominant) hand; then another three on departure day, and a third set a week later, which they mailed in. As the workshop progressed, we swabbed raw ingredients, starters, and the ferments once they got going. I did more swabbing after everyone left, then mailed all the samples back to the lab.

Student Lauren Rhoades making kimchi.

Student Lauren Rhoades making kimchi.


Fermented daikon radish black-eyed pea natto, and other fermented delicacies served with lunch at Walnut Ridge.

Fermented daikon radish black-eyed pea natto, and other fermented delicacies served with lunch at Walnut Ridge.

I have not yet seen any results of our testing, but I am hoping it can help us better understand the distinctive microbial communities of different traditional fermented foods and how, and how community composition develops over time. And I hope that the testing of the students can help us better understand how eating these microbe-rich foods impacts upon our own microbiomes. I look forward to further collaboration with the American Gut Project, and to better understanding complex microbial communities and the interactions among them.


Sandor Ellix Katz is a fermentation revivalist. His books Wild Fermentation (2003) and the Art of Fermentation (2012), along with the hundreds of fermentation workshops he has taught around the world, have helped to catalyze a broad revival of the fermentation arts. A self ­taught experimentalist who lives in rural Tennessee, the New York Times calls him “one of the unlikely rock stars of the American food scene.” Sandor is the recipient of a James Beard award and many other honors. For more information, check out his website.